The Sosnick Group at The University of Chicago


The Sosnick Group strives to characterize the general principles that guide protein folding and dynamics. We combine multiple experimental and computational approaches to characterize the behavior of proteins in diverse contexts


 

SAXS analysis - collapsed or expanded

Given small angle X-ray scattering (SAXS) dataset for an intrinsically disordered protein (IDP), we have developed an analysis method that can determine both the dimension of the ensemble as well as the quality of the solvent (i.e. the extent of self-interactions in the IDP).

Protein Folding - the 70% Rule

We have found that for many small 2-state proteins, the rate-limiting step of folding - the transition state - has ~70% of the native topology, according to the relative contact order.

 

Molecular Dynamics on your laptop!

Wouldn't it be nice to have physically realistic MD trajectories of protein dynamics without needing cpu-weeks/months of simulations? We have developed an MD engine that can reversibly fold some proteins up to 97 amino acids in cpu-days without requiring the use of fragments, homology or evolution.

Congratulations 12/03/2019

Kourtney Kroll

Congratulations to Kourtney Kroll on winning the David Grier Prize in Innovation in Biophysical Sciences for her project, "Engineering a Light Driven Molecular Motor", in collaboration with the Rock group.

Paper Published 10/30/2019

Zongan WangJohn Jumper

Congratulations to Zongan Wang and John Jumper on having their recent paper published, "On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations", published in BIophysical Journal!

Welcome 07/17/2019

Kourtney Kroll

Welcome to Kourtney Kroll, who is joining our group as a new graduate student

Undergraduate Honors Thesis 04/25/2019

Darren Kahan

Darren Kahan presents his undergraduate honors thesis research!

Protein Folding

Protein Folding

Predicting Folding Dynamics

Predicting Folding Dynamics

Photoswitchable allosteric proteins

Photoswitchable allosteric proteins

Membrane Proteins

Membrane Proteins

Psi analysis

Psi analysis

Conformational Entropy

Conformational Entropy

Z. Wang, J.M. Jumper, K.F. Freed, T.R. Sosnick, "On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations" Biophysical Journal, 117 (2019) 1429-41.

J.A. Riback, M.A. Bowman, A.M. Zmyslowski, K.W. Plaxco, P.L. Clark, T.R. Sosnick, "Commonly used FRET fluorophores promote collapse of an otherwise disordered protein" Proc Natl Acad Sci U S A 116 (2019) 8889-94

J.P. Zayner, T. Mathes, T.R. Sosnick, J.T.M. Kennis, "Helical Contributions Mediate Light-Activated Conformational Change in the LOV2 Domain of Avena sativa Phototropin 1" ACS Omega 2019, 4(1) 1238-43.

J.M. Jumper, N.F. Faruk, K.F. Freed, T.R. Sosnick, "Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics" PLoS Comput Biol 14(12): e1006342

J.M. Jumper, N.F. Faruk, K.F. Freed, T.R. Sosnick, "Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours" PLoS Comput Biol. 14(12): e1006578

Z. Wang, J.M. Jumper, S. Wang, K.F. Freed, T.R. Sosnick, "A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations." Biophysical Journal, 115 (2018) 1872-84.

University of Chicago
Biochemistry & Molecular Biophsyics
Biophysical Sciences
Institute for Molecular Engineering
Institute for Biophysical Dynamics